--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hmdb/lib/conf.pm	Thu Jan 28 10:52:26 2016 -0500
@@ -0,0 +1,259 @@
+package lib::conf ;
+
+use strict;
+use warnings ;
+use Exporter ;
+use Carp ;
+use Data::Dumper ;
+
+use vars qw($VERSION @ISA @EXPORT %EXPORT_TAGS);
+
+our $VERSION = "1.0" ;
+our @ISA = qw(Exporter) ;
+our @EXPORT = qw( as_conf get_value_from_conf check_path_and_file ) ;
+our %EXPORT_TAGS = ( ALL => [qw( as_conf get_value_from_conf )] ) ;
+
+=head1 NAME
+
+conf - A module for manage pfem conf file
+
+=head1 SYNOPSIS
+
+    use conf ;
+    my $object = conf->new() ;
+
+=head1 DESCRIPTION
+
+This module does manage conf file (extract all or selected fields)
+
+=head1 METHODS
+
+Methods are :
+
+=head2 METHOD new
+
+	## Description : new
+	## Input : $self
+	## Ouput : bless $self ;
+	## Usage : new() ;
+
+=cut
+## START of SUB
+sub new {
+    ## Variables
+    my $self={};
+    bless($self) ;
+    return $self ;
+}
+### END of SUB
+
+=head2 METHOD as_conf
+
+	## Description : permet de cr�er l'object conf � partir d'un fichier de conf de type KEY=VALUE
+	## Input : $file
+	## Ouput : $oConf (a hash)
+	## Usage : my ( $oConf ) = as_conf( $file ) ;
+	
+=cut
+## START of SUB
+sub as_conf {
+	## Retrieve Values
+    my $self = shift ;
+    my ( $file, $separator ) = @_ ;
+    
+#    if (!defined $separator) { $separator = ';' } ## set separator to ;
+    
+    if ( !defined $file )  {  croak "Can't create object with an none defined file\n" ; }
+    
+    my %Conf = () ; ## Hash devant contenir l'ensemble des parametres locaux
+	
+	if (-e $file) {
+		open (CFG, "<$file") or die "Can't open $file\n" ;
+		while (<CFG>) {
+			chomp $_ ;
+			if ( $_ =~ /^#(.*)/)  {	next ; }
+			elsif ($_ =~/^(\w+?)=(.*)/) { ## ALPHANUMERIC OR UNDERSCORE ONLY FOR THE KEY AND ANYTHING ELSE FOR VALUE
+				
+				my ($key, $value) = ($1, $2) ;
+				
+				if (defined $separator) {
+					if ( $value=~/$separator/ ) { ## is a list to split
+						my @tmp = split(/$separator/ , $value) ;
+						$Conf{$key} = \@tmp ;
+					}
+				}
+				else {
+					$Conf{$key} = $value ;
+				}
+			}
+		}
+		close(CFG) ;
+	}
+	else { 
+		croak "Can't create object with an none existing file\n" ;
+	}
+	
+    return ( \%Conf ) ;
+}
+## END of SUB
+
+=head2 METHOD as_conf_list
+
+	## Description : permet de charger une liste txt en array
+	## Input : $file
+	## Output : elements
+	## Usage : my ( elements ) = as_conf_list( $conf_file ) ;
+	
+=cut
+## START of SUB
+sub as_conf_list {
+	## Retrieve Values
+    my $self = shift ;
+    my ( $file ) = @_ ;
+    
+    my @elements = () ;
+    if ( !defined $file )  {  croak "Can't create object with an none defined file\n" ; }
+    
+    if (-e $file) {
+		open (CFG, "<$file") or die "Can't open $file\n" ;
+		while (<CFG>) {
+			chomp $_ ;
+			if ( $_ =~ /^#(.*)/)  {	next ; }
+			elsif ($_ =~/^(.*)/) { if (defined $1) { push (@elements, $1) ; } 	}
+		}
+    }
+    else {
+		croak "Can't create object with an none existing file\n" ;
+	}
+    return(\@elements) ;
+}
+## END of SUB
+
+=head2 METHOD get_value_from_conf
+
+	## Description : permet de retourner une valeur du hash de conf � partir d'une key
+	## Input : $oConf, $Key
+	## Ouput : $Value
+	## Usage : my ( $Value ) = get_value_from_conf( $oConf, $Key ) ;
+	
+=cut
+## START of SUB
+sub get_value_from_conf {
+	## Retrieve Values
+    my $self = shift ;
+    my ( $oConf, $Key ) = @_ ;
+    
+    my $Value = undef ;
+    
+    if ( defined $oConf ) {
+    	if ( defined $oConf->{$Key} ) {
+    		$Value = $oConf->{$Key} ;
+    	}
+    }
+    else {
+    	croak "Can't manage value with undefined object\n" ;
+    }
+    return($Value) ;
+}
+## END of SUB
+
+=head2 METHOD get_value_from_conf
+
+	## Description : permet de retourner une valeur du hash de conf � partir d'une key
+	## Input : $oConf, $Key
+	## Ouput : $Value
+	## Usage : my ( $Value ) = get_value_from_conf( $oConf, $Key ) ;
+	
+=cut
+## START of SUB
+sub split_value_from_conf {
+	## Retrieve Values
+    my $self = shift ;
+    my ( $oConf, $Key, $sep ) = @_ ;
+    
+    my $value = undef ;
+    my @values = () ;
+    
+    if ( defined $oConf ) {
+    	if ( defined $oConf->{$Key} ) {
+    		$value = $oConf->{$Key} ;
+    		@values = split ( /$sep/, $value) ;
+    	}
+    }
+    else {
+    	croak "Can't manage value with undefined object\n" ;
+    }
+    return(\@values) ;
+}
+## END of SUB
+
+
+=head2 METHOD check_path_and_file
+
+	## Description : permet de v�rifier les path et la pr�sence des exe d�crits dans le file conf. Bloque le script en cas de probleme
+	## Input : $oConfs
+	## Ouput : NA
+	## Usage : &get_value_from_conf( $oConf ) ;
+	
+=cut
+## START of SUB
+sub check_path_and_file {
+	
+	my $self = shift ;
+	my ( $oConfs ) = @_ ;
+	
+	foreach my $conf ( keys %{ $oConfs } ) {
+		if ( $conf =~ /^FILE/ ) {
+			if ( -e $oConfs->{$conf} ) {
+				if ( -s $oConfs->{$conf} ) { next ; }
+				else { carp "[Warning] : The size of file $oConfs->{$conf} is null\n" ; }
+			}
+			else {
+					carp "[Warning] : The file $oConfs->{$conf} doesn't exist\n" ;
+			}
+		}
+		elsif ( $conf =~ /^PATH/ ) {
+			if ( -d $oConfs->{$conf} ) { next ; }
+			else { carp "[Warning] :  The dir $oConfs->{$conf} doesn't exist\n" ;	}
+		}
+		else { 	next ; 	}
+	}
+	return ;
+}
+## END of SUB
+
+1 ;
+
+
+__END__
+
+=head1 SUPPORT
+
+You can find documentation for this module with the perldoc command.
+
+ perldoc conf.pm
+
+
+=head1 Exports
+
+=over 4
+
+=item :ALL is as_conf get_value_from_conf
+
+=back
+
+=head1 AUTHOR
+
+Franck Giacomoni E<lt>franck.giacomoni@clermont.inra.frE<gt>
+
+=head1 LICENSE
+
+This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
+
+=head1 VERSION
+
+version 1 : 10 / 02 / 2013
+
+version 2 : ??
+
+=cut
\ No newline at end of file